A survey of more than 2,000 11-16s shows that only 14 per cent think school councils make a difference, while one in five did not know if their school had one.
The findings from a poll by Mori, commissioned by Professor Kathleen Marshall, Commissioner for Children and Young People, are part of YouthLink's comprehensive research study, "Being Young in Scotland".
Only 26 per cent of boys said they found it easy to talk to teachers, and just 22 per cent of girls were confident about approaching teachers to discuss school issues. Disabled pupils were the most likely group to make their views known, at 35 per cent.
The YouthLink study is due to be published later this year.
Ronnie Smith, general secretary of the Educational Institute of Scotland, said: "I am surprised by these figures. It's not the impression that our members have - of pupils holding back. Perhaps they do wish to engage, but less on issues to do with the school and more to do with particular issues that relate to their own situation."
Campaigners for children's rights claim the findings show that schools are not working hard enough to involve children or to ensure the council has a high enough profile.
Cathy McCulloch, co-director of the Children's Parliament, said: "I hear stories all the time of how schools are undermining the process. One teacher told me that the school council was just a moaning shop, until she realised her approach encouraged it. When she learnt how to engage the children better it became a more meaningful experience.
"Another teacher said her school council was disbanded because all the children wanted to talk about was the toilets and school dinners. But these things are important to them and if they want to discuss them then the school should listen."
Engaging with children is more than just good policy, it is also a duty, according to the office of the Commissioner for Children and Young People.
"Giving school pupils this say is not optional," said Stephen Bermingham, head of participation.
"Article 12 of the United Nations Convention on the Rights of the Child states that children have the right to express views on all matters affecting them, and the Standards in Scotland's Schools Act 2000 charges education authorities with giving due regard to the 'views of the child or young person in decisions that significantly affect them'."
The research had found pockets of good practice, but much more needed to be done. "Pupils are well placed to advise schools on how they can be more effective in delivering education," Mr Bermingham said. "Giving all children and young people a say in how their school is run will increase their sense of ownership over school decisions and create an ethos that will only improve the low level disruptive behaviour that is prevalent in many schools in Scotland."
The office for the Children's Commissioner and the Children's Parliament both argue that local authorities need to invest more to equip children with the skills to make decisions from an early age.
Currently, young people are showing a strong disinclination to becoming active citizens. In the 2003 YouthLink survey, fewer than half of those questioned thought is was important to vote.